GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion

Cheng, Lixin1; Wu, Haonan1,2; Zheng, Xubin1,3; Zhang, Ning4; Zhao, Pengfei1,2; Wang, Ran1,3; Wu, Qiong5; Liu, Tao6; Yang, Xiaojun4; Geng, Qingshan1,2

2023

10.1093/bioinformatics/btac850

BIOINFORMATICS   影响因子和分区

1367-4803

1367-4811

["Motivation: Many studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear.","Results: We constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status. First, we separately built two gene pair signatures IDH-GPS and 1p/19q-GPS and elucidated that they were useful transcriptome markers projecting from corresponding genome variations. Then, the gene pairs in these two models were assembled to develop an integrated model named Glioma Prognostic Gene Pair Signature (GPGPS), which demonstrated high area under the curves (AUCs) to predict 1-, 3- and 5-year overall survival (0.92, 0.88 and 0.80) of glioma. GPGPS was superior to the single GPSs and other existing prognostic signatures (avg AUC=0.70, concordance index=0.74). In conclusion, the ensemble prognostic signature with 10 gene pairs could serve as an independent predictor for risk stratification and survival prediction in glioma. This study shed light on transferring knowledge from genetic alterations to expression changes to facilitate prognostic studies.","Availability and implementation: Codes are available at https://github.com/Kimxbzheng/GPGPS.git","Contact: easonlcheng@gmail.com or gengqingshan@szhospital.com","Supplementary information: Supplementary data are available at Bioinformatics online."]

SCI

英语

第一 ; 通讯

National Key R&D Program of China[2018YFC2001805] ; Shenzhen Science and Technology Program[JCYJ20220530152409020]

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics

Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability

WOS:001025519200034

OXFORD UNIV PRESS

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Jinan Univ, Clin Med Coll 2, Southern Univ Sci & Technol, Affiliated Hosp 1,Shenzhen Peoples Hosp, Shenzhen 518020, Peoples R China
2.Shenzhen Clin Res Ctr Aging, Dept Geriatr, Shenzhen 518020, Peoples R China
3.Chinese Univ Hong Kong, Dept Comp Sci & Engn, Shatin, Hong Kong, Peoples R China
4.Shantou Univ, Guangdong Prov Key Lab Infect Dis & Mol Immunopat, Coll Med, Shantou 515041, Peoples R China
5.Hong Kong Genome Inst, Shatin, Hong Kong, Peoples R China
6.Int Digital Econ Acad, Shenzhen 518020, Peoples R China

Cheng, Lixin,Wu, Haonan,Zheng, Xubin,et al. GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion[J]. BIOINFORMATICS,2023,39(1).

Cheng, Lixin.,Wu, Haonan.,Zheng, Xubin.,Zhang, Ning.,Zhao, Pengfei.,...&Geng, Qingshan.(2023).GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.BIOINFORMATICS,39(1).

Cheng, Lixin,et al."GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion".BIOINFORMATICS 39.1(2023).